Summary from the authors: inbreeding and management in captive populations

Pacific salmon hatcheries aim to supplement declining wild populations and support commercial and recreational fisheries. However, there are also risks associated with hatcheries because the captive and wild environments are inherently different. It is important to understand these risks in order to maximize the success of hatcheries. Inbreeding, which occurs when related individuals interbreed, is one risk that may inadvertently be higher in hatcheries due to space limitations and other factors. Inbred fish may have reduced fitness and survival compared to non-inbred fish. We quantified inbreeding and its effect on key fitness traits across four generations in two hatchery populations of adult Chinook salmon that were derived from the same source. We utilized recent advancements in DNA sequencing technology, which provide much more precise estimates of inbreeding and its potential effects on fitness. Our results indicate that inbreeding may not be severe in salmon hatcheries, even small ones, provided that appropriate management practices are followed. However, we documented an influence of inbreeding on the phenology of adult spawners, which could have biological implications for individual fitness and population productivity. Our findings provide a better understanding of changes that may occur in hatchery salmon and will further inform research on “best” hatchery practices to minimize potential risks. 

Article: Waters CD, Hard JJ, Fast DE, Knudsen CM, Bosch WJ, Naish KA. 2020. Genomic and phenotypic effects of inbreeding across two different hatchery management regimes in Chinook salmon. Molecular Ecology https://doi.org/10.1111/mec.15356.

Summary from the authors: Individualized mating system estimation using genomic data

Mimulus guttatus

Hermaphroditic species of plants and animal can produce a mixture of outcrossed and self-fertilized offspring. Estimating the relative frequency of these two outcomes, i.e. the outcrossing rate, has been a major focus in the evolutionary study of reproductive strategies. Outcrossing rate is also a key parameter for plant breeding and for conservation efforts. This paper generalizes a Bayesian method to estimate outcrossing rate (BORICE) using genomic data. Application of the program to an experimental study of Mimulus guttatus illustrates estimation (10% of progeny were selfed), and also how inference of mating system parameters can set up “downstream” evolutionary studies. In the Mimulus study, these downstream analyses included pollination biology (the genetic composition of pollen changed over the season) and local adaptation (inversion polymorphisms exhibit unique patterns of micro spatial structure within the population).

-Professor John K Kelly, University of Kansas

Full article: Colicchio, J., Monnahan, P. J., Wessinger, C. A., Brown, K., Kern, J. R., & Kelly, J. K. (2020). Individualized mating system estimation using genomic data. Molecular ecology resources. https://doi.org/10.1111/1755-0998.13094

Summary from the authors: telomere length predicts remaining lifespan

Close-up of an adult common tern with its prey. Photo credit: Andrea Parisi

Telomeres are DNA structures located at the end of chromosomes. They protect the chromosome, but shorten at each cell division. When telomeres get too short, the normal functioning of cells can be impaired. An individual’s telomere length may therefore predict its future lifespan, and understanding individual telomere dynamics could help to understand ageing in general.

Telomere shortening can be accelerated due to stress, thereby acting as a biomarker of an individual’s health status. However, some studies suggest that individual differences in telomere length are already determined at birth, and largely consistent over life.

We investigated individual telomere dynamics in a long-lived seabird, the common tern. The telomere lengths of 387 individuals, aged from 2 to 24 years, were repeatedly sampled across 10 years. We found that an individual’s telomeres shortened as they got older. Telomere shortening was also slightly increased if individuals had produced more chicks in the previous year. However, the correlation between repeated measures of an individual’s telomere length was very high, even with 6 years between measures. Nevertheless, an individual’s telomere length positively predicted its remaining lifespan, leaving the question of whether lifespan is already partly determined at the start of life.

Full article: Bichet C, Bouwhuis S, Bauch C, Verhulst S, Becker PH, Vedder O. 2019. Telomere length is repeatable, shortens with age and reproductive success, and predicts remaining lifespan in a long-lived seabird. Molecular ecology. https://doi.org/10.1111/mec.15331

Summary from the authors: genetic architecture of sexual dimorphism in an interspecific cross

The evolution of differences among females and males or sexual dimorphism (SD) is very common in animals but rare in plants. These differences emerge because there is a conflict of interests between sexes to maximize their reproductive success. Thus,  moving genes of reproductive traits to low recombining regions such as the sex chromosomes might be one way to solve this conflict at the genomic level. Closely related species with young sex chromosomes, which differ in the degree of SD, are ideal systems to explore the underlining genetic architecture of SD. We have crossed a female from Silene latifolia with marked SD with a male from S. dioica with less SD. We performed a QTL analysis of reproductive and vegetative traits in the F2 hybrids to find out if sexually dimorphic traits are located on the sex chromosomes, and how they contribute to species differences. Our results support that evolutionary young sex chromosomes are important for the expression of both SD and species differences. Moreover, transgressive segregation (traits with extreme values) and a reversal of SD in the F2s indicated that SD is constrained within the species but not in the recombinant hybrids. Sexual selection can, thus, contribute to speciation.

Full article: Baena-Díaz F, Zemp N, Widmar A. 2019. Insights into the genetic architecture of sexual dimorphism from an interspecific cross between two diverging Silene (Caryophyllaceae) species. Molecular ecology. https://doi.org/10.1111/mec.15271

Summary from the authors: City life alters the gut microbiome and stable isotope profiling of the eastern water dragon (Intellagama lesueurii)

Whilst urbanisation poses a major threat to many species, there is growing evidence to suggest that some species, labelled ‘urban adapters’, are thriving within the urban landscape. Urban landscapes differ drastically from native habitats, where urban adapters are often exposed to a more diverse range of novel food items compared to their rural counterparts, which frequently includes human subsidised resources. Diet is one of the most important factors influencing the gut microbiome, an extremely influential symbiotic community that plays a critical role in many processes affecting host health and fitness, including metabolism, nutrition, immunology and development. Here, using populations of the eastern water dragon in Queensland, Australia, we explore the link between urbanisation, diet and gut microbial changes. We show that city dragons exhibit a more diverse gut microbiome than their rural counterparts, and display microbial signatures of a diet that is richer in plant-material and higher in fat. Elevated levels of the Nitrogen-15 isotope in the blood of city dragons also suggests their diet may be richer in protein. These results highlight that urbanisation can have pronounced effects on the gut microbial communities of wild animals, but we do not yet know the possible repercussions of these microbial changes.

Full article: Littleford‐Colquhoun BL, Weyrich LS, Kent N, Frere CH. City life alters the gut microbiome and stable isotope profiling of the eastern water dragon (Intellagama lesueurii). Mol Ecol. 2019;28:4592–4607. https://doi.org/10.1111/mec.15240

Summary from the authors: Host plant associations and geography interact to shape diversification in a specialist insect herbivore

The sexual generation female of the cynipid gall wasp Belonocnema treatae, which forms locally adapted populations on three closely related live oaks across the southeastern United States. Photo credit: Jena Johnson.

In this study, we wanted to know how geography and ecology predicted population genetic structure among 58 populations of the gall wasp Belonocnema treatae, which exhibits regional specialization on three host plant species across the U.S. Gulf Coast. We combined range-wide sampling with a genotype-by-sequencing approach for 40,699 SNPs across 1,217 individuals. Disentangling the processes underlying geographic and environmental patterns of biodiversity is challenging, as such patterns emerge from eco‐evolutionary processes confounded by spatial autocorrelation among sample units. We evaluated this question using a hierarchical Bayesian model (ENTROPY) to assign individuals to genetic clusters and estimate admixture proportions. Using distance-based Moran’s eigenvector mapping, we generated regression variables that represent varying degrees of spatial autocorrelation in genetic variation among sample sites. These spatial variables, along with host association, were incorporated in distance-based redundancy analysis (dbRDA) to partition the relative contributions of host plant and spatial autocorrelation. This novel approach of combining ENTROPY results with dbRDA to analyze SNP data unveiled a complex mosaic of diversification within and among insect populations forming discrete host associated lineages coupled with geographic variation. This demonstrates that geography and ecology play significant roles in explaining patterns of genomic variation in B. treatae – an emerging model of ecological speciation.

Full article: Driscoe AL, Nice CC, Busbee RW,Hood GR, Egan SP, Ott JR. Host plant associations and geography interact to shape diversification in a specialist insect herbivore. Mol Ecol. 2019;28:4197–4211. https://doi.org/10.1111/mec.15220

Summary from the authors: Polygenic selection drives the evolution of convergent transcriptomic landscapes across continents within a Nearctic sister-species complex

Lake Whitefish (Coregonus clupeaformis)
Adult size benthic (normal) and limnetic (dwarf) sympatric whitefish
Sampled from Cliff Lake, Maine, USA.
Illustration by Paul Vecsei.

The Lake Whitefish (Coregonus clupeaformis) is found in Nearctic post-glacial freshwater lakes, and diverged about 500,000 years ago from its sister species, the European Whitefish (Coregonus lavaretus) found throughout Northern Europe, European Alpine lakes and Russia. These two lineages underwent an adaptive radiation following the last glaciation, resulting in the sympatric occurrence of limnetic and benthic species-pairs. Decades of research has aimed to decipher the process of adaptive divergence and ecological speciation in the Whitefish species complex. Here, we compared independent diverging species-pairs from the two continents to elucidate the genomic and transcriptomic bases associated with the benthic-limnetic diversification. We used a statistical framework to detect polygenic targets of selection associated with phenotypic diversification. We identified a subset of genes that showed convergent patterns of differential expression between limnetic and benthic species across both continents. Those adaptive divergent genes retained a higher degree of shared polymorphism among species-pairs, most likely due to balancing selection, and this genetic variation was associated with changes in levels of gene expression between species. As such, our results indicate that standing genetic variation underlying phenotypes involved in the ecological speciation of the whitefish species-pairs has been partly maintained in parallel across both continents for at least half a million years.

-Clément Rougeux – Postdoctoral Researcher, University of Calgary

Full article: Rougeux C, Gagnaire P‐A, Praebel K, Seehausen O, Bernatchez L. Polygenic selection drives the evolution of convergent transcriptomic landscapes across continents within a Nearctic sister species complex. Mol Ecol. 2019;28:4388–4403. https://doi.org/10.1111/mec.15226